Related papers: Reconstructing DNA copy number by joint segmentati…

Several genetic alterations are involved in the genesis and development of cancers. The determination of whether and how each genetic alterations contributes to cancer development is fundamental for a complete understanding of the human…

Motivation: Array Comparative Genomic Hybridization (aCGH) is used to scan the entire genome for variations in DNA copy number. A central task in the analysis of aCGH data is the segmentation into groups of probes sharing the same DNA copy…

Array comparative genomic hybridization(CGH) is a high resolution technique to assess DNA copy number variation. Identifying breakpoints where copy number changes will enhance the understanding of the pathogenesis of human diseases, such as…

Mining gene expression profiles has proven valuable for identifying signatures serving as surrogates of cancer phenotypes. However, the similarities of such signatures across different cancer types have not been strong enough to conclude…

Identifying genes underlying cancer development is critical to cancer biology and has important implications across prevention, diagnosis and treatment. Cancer sequencing studies aim at discovering genes with high frequencies of somatic…

Identifying the genes and mutations that drive the emergence of tumors is a major step to improve understanding of cancer and identify new directions for disease diagnosis and treatment. Despite the large volume of genomics data, the…

Motivation: As cancer researchers have come to appreciate the importance of intratumor heterogeneity, much attention has focused on the challenges of accurately profiling heterogeneity in individual patients. Experimental technologies for…

We present a calculation technique for modeling inhomogeneous DNA replication kinetics, where replication factors such as initiation rates or fork speeds can change with both position and time. We can use our model to simulate data sets…

BACOM is a statistically principled and unsupervised method that detects copy number deletion types (homozygous versus heterozygous), estimates normal cell fraction, and recovers cancer specific copy number profiles, using allele specific…

The study of genomic variation has provided key insights into the functional role of mutations. Predominantly, studies have focused on single nucleotide variants (SNV), which are relatively easy to detect and can be described with rich…

A major challenge for cancer pathologists is to determine whether a new tumor in a patient with cancer is a metastasis or an independent occurrence of the disease. In recent years numerous studies have evaluated pairs of tumor specimens to…

DNA storage has emerged as an important area of research. The reliability of DNA storage system depends on designing the DNA strings (called DNA codes) that are sufficiently dissimilar. In this work, we introduce DNA codes that satisfy a…

Understanding the dynamics of genome rearrangements is a major issue of phylogenetics. Phylogenetics is the study of species evolution. A major goal of the field is to establish evolutionary relationships within groups of species, in order…

DNA copy number and mRNA expression are widely used data types in cancer studies, which combined provide more insight than separately. Whereas in existing literature the form of the relationship between these two types of markers is fixed a…

Tumor cells acquire different genetic alterations during the course of evolution in cancer patients. As a result of competition and selection, only a few subgroups of cells with distinct genotypes survive. These subgroups of cells are often…

Despite initial success, cancer therapies often fail due to the emergence of drug-resistant cells. In this study, we use a mathematical model to investigate how cancer evolves over time, specifically focusing on the state of the tumor when…

Changepoint detection methods are used in many areas of science and engineering, e.g., in the analysis of copy number variation data, to detect abnormalities in copy numbers along the genome. Despite the broad array of available tools,…

Background: DNA, RNA, and protein sequence motifs can be recognition sites for biological functions such as regulation, DNA base modification, and molecular binding in general. The gain and loss of such motifs can carry important…

The rapid growth of cancer genome structural information provides an opportunity for a better understanding of the mutational mechanisms of genomic alterations in cancer and the forces of selection that act upon them. Here we test the…

Extracting genetic information from a full range of sequencing data is important for understanding diseases. We propose a novel method to effectively explore the landscape of genetic mutations and aggregate them to predict cancer type. We…